LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# sample surface deposition script for molecules

units		lj
atom_style      bond
boundary        p p f

lattice		fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region          box block 0 5 0 5 0 10
create_box      3 box bond/types 1 extra/bond/per/atom 1
Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
  1 by 1 by 1 MPI processor grid

region		substrate block INF INF INF INF INF 3
create_atoms	1 region substrate
Created 350 atoms
  Time spent = 0.000686646 secs

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0
pair_coeff	1 2 1.0 1.0 5.0
mass		* 1.0

bond_style	harmonic
bond_coeff      1 5.0 1.0

neigh_modify	delay 0

group		addatoms type 2
0 atoms in group addatoms
region          mobile block 0 5 0 5 2 INF
group		mobile region mobile
150 atoms in group mobile

compute		add addatoms temp
compute_modify	add dynamic/dof yes extra/dof 0

fix		1 addatoms nve
fix		2 mobile langevin 0.1 0.1 0.1 587283
fix		3 mobile nve

molecule        dimer molecule.dimer
Read molecule dimer:
  2 atoms with max type 3
  1 bonds with max type 1
  0 angles with max type 0
  0 dihedrals with max type 0
  0 impropers with max type 0
region          slab block 0 5 0 5 8 9
fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0                 mol dimer vz -1.0 -1.0
fix		5 addatoms wall/reflect zhi EDGE

thermo_style	custom step atoms temp epair etotal press
thermo          100
thermo_modify	temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

#dump		1 all atom 50 dump.deposit.atom

#dump		2 all image 50 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	2 pad 5

#dump		3 all movie 50 movie.mpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	3 pad 5

run             10000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.3
  ghost atom cutoff = 5.3
  binsize = 2.65, bins = 3 3 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.152 | 4.152 | 4.152 Mbytes
Step Atoms Temp E_pair TotEng Press 
       0      350            0   -6.9215833   -6.9215833   -1.0052629 
     100      352   0.83994737   -6.8875167   -6.8803581  -0.73353914 
     200      354   0.83994737   -6.8593854    -6.845149  -0.70414703 
     300      356   0.84169616   -6.8174189   -6.7961324  -0.69200581 
     400      358   0.84705847    -6.785416   -6.7570071  -0.70386101 
     500      360   0.87562973   -6.7507562    -6.714217  -0.68491831 
     600      362   0.89546097   -6.7133515   -6.6684358  -0.68373096 
     700      364   0.86923875   -6.6724351   -6.6215093   -0.6663574 
     800      366   0.93007871   -6.6448092   -6.5816911  -0.68706422 
     900      368    1.0020611   -6.6164541    -6.540933  -0.66074734 
    1000      370    1.0082042   -6.5845669   -6.5014101  -0.69453732 
    1100      372   0.96783727   -6.5649235   -6.4753076   -0.6717256 
    1200      374   0.97597749   -6.5935771   -6.4925926  -0.69360182 
    1300      376   0.80208918   -6.5923852   -6.5033139  -0.64868248 
    1400      378   0.66705029    -6.582928   -6.5082634   -0.6111322 
    1500      380   0.67555528   -6.5640796   -6.4816473  -0.67638117 
    1600      382   0.65916245    -6.551728   -6.4662574  -0.62833932 
    1700      384     0.718469   -6.5624935   -6.4643654  -0.64737567 
    1800      386   0.59257091   -6.5604373   -6.4675604  -0.61982866 
    1900      388   0.63118529   -6.5638788    -6.467728  -0.63403973 
    2000      390    0.6013361    -6.571937    -6.473428  -0.62753885 
    2100      392   0.48508625   -6.5519559   -6.4663394  -0.66580902 
    2200      394   0.50266444   -6.5357335   -6.4395422  -0.71780255 
    2300      396   0.52557785   -6.5469569   -6.4355521  -0.65421156 
    2400      398   0.66055178   -6.5509266   -6.4186172  -0.65273326 
    2500      400   0.69210544   -6.5578062   -6.4211169  -0.68232818 
    2600      402   0.64576434   -6.6050398   -6.4574266  -0.64849208 
    2700      404   0.56298016   -6.6350083    -6.503562    -0.746185 
    2800      406   0.49149694   -6.6482516   -6.5155551  -0.76320999 
    2900      408   0.48366321   -6.6606024   -6.5257882  -0.65612432 
    3000      410   0.47356141   -6.6756446   -6.5312692  -0.70811639 
    3100      412   0.47568619   -6.6934709   -6.5474974  -0.72316681 
    3200      414   0.38708973   -6.6932142   -6.5659264  -0.73056797 
    3300      416   0.43665017   -6.6999962   -6.5567504  -0.75890315 
    3400      418   0.34923989   -6.7185629   -6.5909531  -0.66986444 
    3500      420   0.33999089   -6.6922536   -6.5729709  -0.70698979 
    3600      422      0.37659   -6.6827522   -6.5521249  -0.68796169 
    3700      424   0.34150483   -6.6973468   -6.5698573  -0.68312043 
    3800      426   0.41110243   -6.7043016   -6.5510735  -0.71352712 
    3900      428   0.40957994   -6.7172729   -6.5557011  -0.70233721 
    4000      430   0.42723175   -6.7170007   -6.5537357   -0.7497547 
    4100      432   0.37176212   -6.7218812   -6.5574518   -0.7098714 
    4200      434   0.33265381   -6.7082458   -6.5637164  -0.70399102 
    4300      436   0.43029564   -6.7142231   -6.5431037  -0.76230436 
    4400      438   0.38216708   -6.7315576   -6.5614315   -0.6674734 
    4500      440   0.35981631   -6.7496554    -6.583264  -0.73404044 
    4600      442   0.36073617   -6.7479258   -6.5907772  -0.71067075 
    4700      444   0.35705292   -6.7678184   -6.5973053  -0.75325156 
    4800      446   0.37426281   -6.7869581   -6.6010006  -0.67542828 
    4900      448   0.33524109   -6.7800476   -6.6026334  -0.66398211 
    5000      450   0.31770101   -6.7884069   -6.6064017  -0.74655689 
    5100      452   0.31791473   -6.7695361   -6.5901194  -0.77591531 
    5200      454   0.37320367   -6.7756559   -6.5809165  -0.76247336 
    5300      456   0.32228579   -6.7786007   -6.5856918  -0.67574614 
    5400      458   0.31274193   -6.7828483   -6.5928063  -0.72466782 
    5500      460   0.30708694   -6.7858555   -6.5973813  -0.76883863 
    5600      462   0.32849848   -6.7983978   -6.6021343  -0.76855876 
    5700      464   0.35124617   -6.8131288   -6.5975496  -0.78865946 
    5800      466   0.35055399   -6.8184367   -6.6060092  -0.70530424 
    5900      468   0.33326299   -6.8299034   -6.6095077  -0.68840817 
    6000      470   0.40104727   -6.8633145   -6.6132375  -0.77187971 
    6100      472   0.29105598   -6.8410097   -6.6311104   -0.7715889 
    6200      474   0.30288813   -6.8634336   -6.6428858  -0.78760673 
    6300      476   0.34293767   -6.9005784   -6.6534079  -0.74817698 
    6400      478   0.34963015   -6.9292987    -6.666687  -0.71175243 
    6500      480     0.319367   -6.9395521   -6.6743587  -0.76432283 
    6600      482   0.29016877   -6.9324045    -6.679475  -0.90715919 
    6700      484   0.35436305   -6.9551643   -6.6789059  -0.79939008 
    6800      486     0.327512   -6.9608693    -6.687362  -0.70392295 
    6900      488   0.32349315   -6.9513424   -6.6847712  -0.75205809 
    7000      490   0.35355467   -6.9907283   -6.7038887  -0.80881264 
    7100      492   0.32140685   -6.9979325   -6.7169278  -0.68673022 
    7200      494   0.32242041   -7.0116346    -6.728848  -0.79432529 
    7300      496   0.26266524   -6.9966902   -6.7334152  -0.86050198 
    7400      498   0.31564904   -7.0133015   -6.7158904  -0.81615792 
    7500      500   0.36973921   -7.0516561    -6.717083  -0.79423832 
    7600      502   0.33599186   -7.0516408   -6.7296713  -0.83610882 
    7700      504   0.29691416   -7.0495062    -6.738076  -0.83634675 
    7800      506    0.3244215   -7.0434148   -6.7342677   -0.7170135 
    7900      508   0.29167542   -7.0637209   -6.7576924  -0.78857188 
    8000      510   0.34198998   -7.1041546   -6.7635656  -0.83376311 
    8100      512   0.33068905   -7.1341746   -6.7960028  -0.78639771 
    8200      514   0.29688969    -7.136245   -6.8093036  -0.85753154 
    8300      516   0.29829676   -7.1313196   -6.8076328  -0.76960702 
    8400      518   0.31096049   -7.1559166   -6.8202327  -0.72775356 
    8500      520   0.26677854   -7.1413516   -6.8361967  -0.81908087 
    8600      522   0.28811568   -7.1390821   -6.8248702  -0.88515896 
    8700      524   0.27520272   -7.1501541   -6.8311651  -0.81462692 
    8800      526   0.28763152   -7.1525343   -6.8281253  -0.74124759 
    8900      528   0.29917883   -7.1547953   -6.8229151  -0.81440712 
    9000      530   0.28474306   -7.1612717   -6.8236771  -0.79150099 
    9100      532   0.29409713   -7.1748026   -6.8272211   -0.7916524 
    9200      534   0.26767862   -7.1646362   -6.8313179  -0.79362392 
    9300      536   0.27111075   -7.1719185   -6.8399556   -0.9578129 
    9400      538   0.33952348    -7.207044   -6.8368639  -0.89888939 
    9500      540    0.3284439   -7.2371916   -6.8625844   -0.7659201 
    9600      542   0.31256223   -7.2266123   -6.8655682  -0.82722861 
    9700      544   0.30268239   -7.2315617   -6.8705788  -0.81448482 
    9800      546   0.26835398   -7.2214231   -6.8757262  -0.86029096 
    9900      548   0.31676744    -7.264604    -6.884266  -0.74053962 
   10000      550   0.31368419   -7.2759575   -6.8979611  -0.76153366 
Loop time of 7.42799 on 1 procs for 10000 steps with 550 atoms

Performance: 581583.611 tau/day, 1346.258 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.1961     | 4.1961     | 4.1961     |   0.0 | 56.49
Bond    | 0.011222   | 0.011222   | 0.011222   |   0.0 |  0.15
Neigh   | 2.8258     | 2.8258     | 2.8258     |   0.0 | 38.04
Comm    | 0.20406    | 0.20406    | 0.20406    |   0.0 |  2.75
Output  | 0.0014198  | 0.0014198  | 0.0014198  |   0.0 |  0.02
Modify  | 0.14606    | 0.14606    | 0.14606    |   0.0 |  1.97
Other   |            | 0.04341    |            |       |  0.58

Nlocal:    550 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    2349 ave 2349 max 2349 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    39710 ave 39710 max 39710 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 39710
Ave neighs/atom = 72.2
Ave special neighs/atom = 0.363636
Neighbor list builds = 877
Dangerous builds = 0
Total wall time: 0:00:07
